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- PDB-3tvo: Human Carbonic Anhydrase II Proton Transfer Double Mutant -

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Basic information

Entry
Database: PDB / ID: 3tvo
TitleHuman Carbonic Anhydrase II Proton Transfer Double Mutant
ComponentsCarbonic anhydrase 2
KeywordsLYASE / globular protein
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase ...Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMikulski, R.M.
CitationJournal: Biochemistry / Year: 2013
Title: Water Networks in Fast Proton Transfer during Catalysis by Human Carbonic Anhydrase II.
Authors: Mikulski, R. / West, D. / Sippel, K.H. / Avvaru, B.S. / Aggarwal, M. / Tu, C. / McKenna, R. / Silverman, D.N.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2263
Polymers29,0691
Non-polymers1582
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.095, 41.129, 72.100
Angle α, β, γ (deg.)90.000, 104.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29068.809 Da / Num. of mol.: 1 / Mutation: Y7F/N67Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.25 M sodium citrate, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2010 / Details: osmic mirror
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→26.614 Å / Num. all: 31717 / Num. obs: 31717 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Χ2: 1.144 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.663.60.47331431.191199.8
1.66-1.723.70.37531581.181100
1.72-1.83.70.27931701.194199.9
1.8-1.93.70.20831471.192199.8
1.9-2.023.70.15631521.1921100
2.02-2.173.80.12931811.1871100
2.17-2.393.90.1131551.105199.8
2.39-2.7440.09231821.054199.9
2.74-3.4540.07632051.158199.6
3.45-26.61440.06632361.012198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.3_467refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TBT

1tbt


Resolution: 1.6→26.614 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.8692 / SU ML: 0.21 / σ(F): 0 / σ(I): 0 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1934 6.3 %RANDOM
Rwork0.1661 ---
obs0.1686 30707 96.49 %-
all-31717 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.864 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 88.32 Å2 / Biso mean: 24.9706 Å2 / Biso min: 9.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.361 Å2-0 Å2-1.6846 Å2
2---5.0051 Å20 Å2
3---5.3661 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 7 309 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062290
X-RAY DIFFRACTIONf_angle_d1.0193135
X-RAY DIFFRACTIONf_chiral_restr0.074332
X-RAY DIFFRACTIONf_plane_restr0.005409
X-RAY DIFFRACTIONf_dihedral_angle_d12.197881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.65680.46441760.42712623279989
1.6568-1.72320.37251840.31832738292293
1.7232-1.80160.28461820.23442838302095
1.8016-1.89650.23131940.17582833302796
1.8965-2.01530.22021900.15372890308097
2.0153-2.17080.23771980.15632930312899
2.1708-2.38920.20321920.15722927311999
2.3892-2.73460.21182030.16032968317199
2.7346-3.44410.20132100.15522994320499
3.4441-26.6140.14942050.14263032323799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01170.0122-0.010.1539-0.050.0196-0.06780.0561-0.3191-0.0258-0.1289-0.13-0.01940.12910.10940.12320.01090.05820.2569-0.00740.32757.1464-5.980210.559
20.1332-0.26840.17620.5762-0.2190.7643-0.1278-0.1594-0.01720.09810.0904-0.1030.05370.0393-0.00620.14150.01530.00430.173-0.01090.136-4.1725-2.610327.3839
30.6405-0.3025-0.22090.43380.43140.53640.0689-0.02590.1701-0.1818-0.0070.0341-0.1907-0.0185-0.02480.17480.0032-0.02230.1001-0.00120.15-16.89196.890512.987
40.36050.0009-0.00830.32890.1770.208-0.0182-0.0153-0.0149-0.08290.02250.0189-0.03720.0022-0.00240.1289-0.00460.00450.1096-0.00030.11-10.1392-3.554113.2261
50.55070.0077-0.05890.3029-0.03160.01-0.1132-0.19680.05530.1920.13260.07630.1682-0.0821-0.01240.195-0.0160.00960.2585-0.03050.1678-11.9169-3.359234.4273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain X and resid 4:9X4 - 9
2X-RAY DIFFRACTION2chain X and resid 10:45X10 - 45
3X-RAY DIFFRACTION3chain X and resid 46:87X46 - 87
4X-RAY DIFFRACTION4chain X and resid 88:251X88 - 251
5X-RAY DIFFRACTION5chain X and resid 252:261X252 - 261

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